Micro-aeration enhances anaerobic digestion (AD) by accelerating hydrolysis and increasing hydrolytic enzyme activity. Our previous work showed that maintaining the oxidation-reduction potential (ORP) at −470 mV can stimulate the metabolism of the facultative bacterium Proteiniphilum, promoting acetate production for acetoclastic methanogenesis. This increased methane yield from 22.9 to 78.1 NmL/gVS at an organic loading rate of 5.0 g VS/L/day. However, how micro-aeration drives these improvements at pathway level remains unclear. Identifying the key enzymes and metabolic pathways controlling this response would enable more effective AD performance. To address this, we integrated genomics and transcriptomics to construct pathway networks during micro-aerated AD. Using computational techniques, including the Greedy Peel Algorithm and Gaussian Boson Sampling (GBS), we identified highly interconnected enzyme groups within these networks, indicating the specific pathways that are critical to the process enhancements. The results showed that pyruvate dehydrogenase is a key driver catalysing pyruvate conversion to acetate, aligning with the observed increase in acetate concentrations. As this enzyme is redox sensitive, optimising micro-aeration rates can enhance process performance. ATP synthase was also identified as important, suggesting that adequate pH buffering is required to maintain the proton gradient for ATP synthesis. These findings offer mechanistic insights for optimising micro-aerated AD. They also demonstrate the potential of GBS, a quantum computing approach, in advancing bioprocess engineering, such as AD of sewage sludge and lignocellulosic biomass.